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<h1>Lab Notes - September</h1>

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<h1>Biobrick Group</h1>
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<h1>Week9</h1>


<table id="notesheet" width="691" border="1" cellspacing="0"
	cellpadding="1">
	<tr>
		<td width="68"><strong>Day</strong></td>
		<td width="612"><strong>Note</strong></td>
	</tr>

	<tr>
		<td id="sheetleft">Aug.29th Monday</td>
		<td width="613">
		<table id="intable" width="561" border="0" cellspacing="0"
			cellpadding="1">

			<td width="260">• Meeting. Summarize all the experiment work so
			far.</td>


			<td width="297">• Cut: 22M(X+P), 1C3(E+P)</td>


		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.30th Tuesday</td>
		<td width="613">
		<table id="intable" width="615" border="0" cellspacing="0"
			cellpadding="1">




		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.31st Wednesday</td>
		<td width="613">
		<table width="563" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="361">• Cut vgb+YFP+tetR, fdhF+RFP+tetR.<br />
				• Run the digestion results</td>
				<td width="198">• Culture the positive results</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Sept.1st Thursday</td>
		<td width="613">
		<table width="572" border="0" cellspacing="0" cellpadding="1">
			<tr>

				<td width="171">• Miniprep: Y#4, R#2/3/4/5<br />
				• Cut Y#4, R#2/3/4/5</td>
				<td width="250">•Run the gel.<br />
				• Send R#3,Y#4 sample to sequencing</td>
				<td width="145">• Hypoxia culture: RFP3, RFP4<br />
				• Preserve Y#4, R#2/3/4/5</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Sept.2nd Friday</td>
		<td width="613">
		<table width="572" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="92">• Phusion PCR</td>
				<td width="276">• Hypoxia Culture: R, Y<br />
				• Run the PCR results. Bands are confirmed right.</td>
				<td width="198">• Purification: vgb, YFP, tetR.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Sept.3rd Saturday</td>
		<td width="613">
		<table width="569" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="152">• Culture: YFP, RFP, A25<br />
				• Culture in micro-oxygen: YFP, RFP, A25</td>
				<td width="149">• Culture in slope medium: RFP, YFP, A25<br />
				• Hypoxia culture: RFP, YFP, A25</td>
				<td width="262">• Check the fluorescence.<br />
				• Neither RFP in hypoxia or oxygen condition. Little YFP both in
				hypoxia and oxygen.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Sept.4th Sunday</td>
		<td width="613">
		<table width="563" height="19" border="0" cellpadding="1"
			cellspacing="0">
			<tr>
				<td width="285">• Miniprep: RFP3, YFP4</td>
				<td width="331">• Cut: RFP3, YFP4, !C3.</td>

			</tr>
		</table>
		</td>
	</tr>

</table>
</p>
<h1>Week10</h1>
<table id="notesheet" width="650" border="1" cellspacing="0"
	cellpadding="1">
	<tr>
		<td width="76"><strong>Day</strong></td>
		<td width="612"><strong>Note</strong></td>
	</tr>

	<tr>
		<td id="sheetleft">Sept.5th Monday</td>
		<td>
		<table id="intable" width="603" border="0" cellspacing="0"
			cellpadding="1">

			<td width="191">• Run the gel: Yu's PCR results, 1C3, RFP3, YFP4<br />
			• Purification: RFP3, YFP4</td>


			<td>• Ligation: RFP3+1C3, YFP4+1C3<br />
			• Hypoxia culture: RFP3, YFP4, A25.</td>
			<td>• Transform the ligation results.<br />
			• Confirmed RFP expression only in hypoxia condition.</td>

		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Sept.6th Tuesday</td>
		<td>
		<table id="intable" width="600" border="0" cellspacing="0"
			cellpadding="1">
			<td width="414">• Check the RFP, YFP plates.</td>
			<td width="182">• Colony PCR</td>

		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Sept.7th Wednesday</td>
		<td>
		<table width="609" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="607">• Culture YFP1/2, RFP3/4</td>

			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Sept.8th Thurday</td>
		<td>
		<table width="597" border="0" cellspacing="0" cellpadding="1">
			<tr>

				<td width="297">• Preserve the strain of RFP1, YFP1/2 in 1C3.<br />
				• Miniprep the remains.</td>
				<td width="140">• Cut: YFP1/2, RFP1</td>
				<td width="154">• Run the digestion results.<br />
				• Culture RFP2</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Sept.9th Friday</td>
		<td>
		<table width="612" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="335">• Miniprep: RFP2, YFP2, RFP1</td>
				<td width="273">• Cut them and run the gel.</td>

			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Sept.10th Saturday</td>
		<td>
		<table width="610" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="161">• Cut YFP(1A3), RFP(1A3) with S+E</td>
				<td width="162">• Purification: RFP(1A3), YFP(1A3)</td>
				<td width="148">• Ligation: RFP+1C3, YFP+1C3</td>
				<td width="131">• Transform the ligation results.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Sept.11th Sunday</td>
		<td>
		<table width="608" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="244">• Check the plates.</td>
				<td width="164">• Culture lig RFY+YFP+IC3<br />
				• Culture 1K3</td>
				<td width="194">• Colony PCR: RFP(1C3)， YFP(1C3)</td>
			</tr>
		</table>
		</td>
	</tr>

</table>

<p>&nbsp;</p>
<h1>Week11</h1>
<table border="1" cellpadding="1" cellspacing="0" id="notesheet3">
	<tr>
		<td width="104"><strong>Day</strong></td>
		<td width="689"><strong>Note</strong></td>
	</tr>
	<tr>
		<td id="sheetleft3">Sept.12th Monday</td>
		<td>
		<table id="intable3" width="603" border="0" cellspacing="0"
			cellpadding="1">
			<tr>
				<td width="191">• Colony PCR: 1A3, 1K3, lig RFP+YFP+1C3.</td>
				<td>• Run the PCR results.</td>
				<td>• Miniprep: lig RFP+YFP+1C3</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft3">Sept.13th Tuesday</td>
		<td>
		<table id="intable3" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td>• Transform 2M, 2I, 6I, 23L.</td>
				<td>• Purification: 1K3</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft3">Sept.14th Wednesday</td>
		<td>
		<table width="600" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td>• Miniprep: 20H, 20J, 22B<br />
				• Cut: 1K3 with E+P, lig3 with S+E,<br />
				12I(CFP) with P+X,</td>
				<td>• Gel excision and /or purification:<br />
				1K3, lig3, 12I(CFP)<br />
				• Culture: <br />
				1I, 1K, 3L, 5E, 7C<br />
				• Run the gel.<br />
				• Miniprep: <br />
				RFP+YFP+1C3.<br />
				</td>
				<td>• Run the gel of<br />
				1K3, lig3, CFP again.<br />
				• Gel excision and purification<br />
				• Ligation:<br />
				Lig3+CFP+1K3</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft3">Sept.15th Thursday</td>
		<td>
		<table width="618" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td>• Preserve: 1I, 1K, 3C, 5E, 7C<br />
				• Transform the ligation results</td>
				<td>• Colony PCR: 2M, 2I，6I，23L<br />
				• Cut: 20H, 20J, 22B with X+P</td>
				<td>• Miniprep: 2M-1, 2I-1, 6I-1, 23L-1<br />
				• Cut: 2M, 2I with E+S</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft3">Sept.16th Friday</td>
		<td>
		<table width="600" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td>• Colony PCR: RFP+YFP+1K3</td>
				<td>• Cut 13K with E+S, <br />
				10I with P+X, 1C3 with E+P<br />
				• Run the gel: <br />
				13K, 10I, 1C3, 2I, 2M, 20J, 22H, 22B</td>
				<td>• Ligation: 13K+10I+1C3<br />
				• Culture: YFP(Amp), CFP(Amp)</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft3">Sept.17th Saturday</td>
		<td>
		<table width="620" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="169">• Order primers for 20H, 20J<br />
				• Culture 20H-1, 20J-1, 22B-1</td>
				<td width="225">• Plate the ligation results<br />
				• Culture RFP+YFP+CFP+1K3</td>
				<td width="220">• Colony PCR: 3A, 1C3<br />
				• Preserve: 1K3, RFP+YFP+1C3.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft3">Sept.18th Sunday</td>
		<td>
		<table width="620" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="120">• Miniprep: 20J, 20H, RFP+YFP+CFP+1K3 1A3]<br />
				• Run the gel of PCR results</td>
				<td>• Cut RFP+YFP+CFP+1K3 with E+P<br />
				• Colony PCR: 13K+10I+1C3<br />
				• PCR: fdhF+rush+Vgb+tetR</td>
				<td></td>
				<td>• Preserve: 20H, 20J, 22B<br />
				• Run the gel: 20H, 20J, 22B<br />
				• Cut the bands and purification.</td>
				<td>• Run the gel: 13K+10I+1C3, RFP+YFP+CFP+1K3<br />
				• Culture: 13K+10I+1C3<br />
				• Grad PCR: fdhF.</td>
			</tr>
		</table>
		</td>
	</tr>
</table>
<p>&nbsp;</p>
<h1>Week12</h1>
<table id="notesheet2" border="1" cellspacing="0" cellpadding="1">
	<tr>
		<td><strong>Day</strong></td>
		<td><strong>Note</strong></td>
	</tr>
	<tr>
		<td id="sheetleft2">Sept.19th Monday</td>
		<td>
		<table id="intable2" width="592" border="0" cellspacing="0"
			cellpadding="1">
			<tr>
				<td width="191">• Miniprep: 13K+10I+1C3, 1C3<br />
				• Run the gel of digestion results.</td>
				<td width="97">• Cut: 13K+10I+1C3, 1A3, fdhF</td>
				<td width="112">• Run the gel: 20H, 20J, rush+vgb, RYC+1K3,
				fdhF, 13K+10I, 1A3</td>
				<td width="94">• Cut and purification: fdhF, 13K+10I, 1A3<br />
				• Culture: CFP, YFP</td>
				<td width="88">• Purification: Rush PCR<br />
				• Cut: 22B with X, rush PCR results with S</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft2">Sept.20th Tuesday</td>
		<td>
		<table id="intable2" width="601" border="0" cellspacing="0"
			cellpadding="1">
			<tr>
				<td width="189">• Run the 20H, 20J from PCR results.<br />
				• Transform: fdhF+13K+10I+1A3</td>
				<td width="122">• Purification: 20B, Rush<br />
				• Ligation: 22B+Rush</td>
				<td width="169">• Purification: ligation results<br />
				• Cut: the ligation results with X+S</td>
				<td width="113">• PCR 20H<br />
				• Self-ligation: rush+22M</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft2">Sept.21st Wednesday</td>
		<td>
		<table width="603" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="276">• Colony PCR: fdhF+13K+10I+1A3 on plates</td>
				<td width="177">• Run the gel of PCR results</td>
				<td width="144">• Culture the positive results.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft2">Sept.22nd Thursday</td>
		<td>
		<table width="611" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="130">• Miniprep: fdhF+13K+10I+1A3<br />
				• Preserve the above.</td>
				<td width="202">• Cut and run the results: fdhF+13K+10I+1A3,
				13K+10I+1C3</td>
				<td width="162">• Cut: RFP with E+S, YFP with X+P, 1K3 with
				E+P, 1C3 with E+P</td>
				<td width="109">• Purification the digestion results.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft2">Sept.23rd Friday</td>
		<td>
		<table width="600" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="376">• Ligate: RFP+1A3/ YFP+1C3/1K3, RFP+1A3/1C3</td>
				<td width="220">• Transform the ligation results.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft2">Sept. 24th Saturday</td>
		<td>
		<table width="604" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="197">• Order primers for 20H, 20J<br />
				• Culture 20H-1, 20J-1, 22B-1</td>
				<td width="200">• Plate the ligation results<br />
				• Culture RFP+YFP+CFP+1K3</td>
				<td width="201">• Colony PCR: 3A, 1C3<br />
				• Preserve: 1K3, RFP+YFP+1C3.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft2">Sept.25th Sunday</td>
		<td>
		<table width="613" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="121">• Miniprep: 20J, 20H, RFP+YFP+CFP+1K3 1A3<br />
				• Run the gel of PCR results</td>
				<td width="116">• Cut RFP+YFP+CFP+1K3 with E+P<br />
				• PCR: fdhF+rush+Vgb+tetR<br />
				• Colony PCR: 13K+10I+1C3</td>
				<td width="66">• Preserve: 20H, 20J, 22B<br />
				• Run the gel: 20H, 20J, 22B<br />
				• Cut the bands and purification.</td>
				<td width="112">• Run the gel: 13K+10I+1C3, RFP+YFP+CFP+1K3<br />
				• Culture: 13K+10I+1C3<br />
				• Grad PCR: fdhF.</td>
			</tr>
		</table>
		</td>
	</tr>
</table>
<p><br />
</p>
</div>
<div id="importantcontainer">
<div class="frame" id="important">
<div class="bgcolors" id="round">
<h1>Biofilm Group</h1>
</div>
<!--bgcolors--></div>
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<p style="clear: both;"></p>
<div id="page2">
<div class="block" id="nsheet">
<h1>3rd Sep</h1>


<p>Directly use DH5α fdhF+RFP colony to inoculate silicone tube set
with 5ml LB. rest for 12h for biofilm attachment.</p>
</div>
<div class="block" id="nsheet">
<h1>4th Sep</h1>
<p>Add 50mlLB+Amp and start circulation.</p>
</div>
<div class="block" id="nsheet">
<h1>6th Sep</h1>
<p>Biofilm with direct inoculation is optimum. Expressed red
florescence but only one small fraction of the biofilm remained after
cutting off the part of the tube.</p>
</div>
<div class="block" id="nsheet">
<h1>12th Sep</h1>
<p>4 silicone tube sets with biofilm attachement time of 3h, 5h,
7.5h and 10h; 4 bubbling sets.</p>
</div>
<div class="block" id="nsheet">
<h1>15th Sep</h1>
<p>The silicone tube set with 3h of attachment achieves optimum
biofilm formation. Bubbling sets glass slides are froze in -80℃ for
later observation with laser confocal. Biofilm formed on glass slide is
about 10μm thick.</p>
</div>
<div class="block" id="nsheet">
<h1>16th Sep</h1>
<p>New sets with silicone tube, a mixture of RFP, CFP and YFP
expressing e.coli. Attachment 3h.</p>
</div>
<div class="block" id="nsheet">
<h1>17th Sep</h1>
<p>Glass slide with bubbling set with the same mixture of e.coli.<br />
Place two filter film on solid culture medium and placed the mixture of
e.coli on the filter to form gas-solid interface biofilm.</p>
</div>
<div class="block" id="nsheet">
<h1>20th Sep</h1>
<p>Observation of glass slide and gas-solid biofilm under laser
confocal. Glass slide are observed directly and gas-solid biofilm is
first pressed by a covering slide so that it would stick to it and
peeled off from the filter for observation.<br />
Biofilm on glass slide is about 8.6μm thick. Biofilm formed on gas-solid
interface is too concentrated in bacteria and culture medium that the
florescence of too strong to see any clear structure.</p>
</div>

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</html>
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        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